Contacts of the helix formed by residues 79 - 100 (chain A) in PDB entry 5VEY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU 4.0 4.7 - - - +
78A LEU* 1.3 96.7 - - + +
80A GLY* 1.3 62.0 + - - +
81A GLU 3.5 2.9 - - - +
82A LEU* 3.6 29.8 - - + -
83A ALA* 2.8 21.5 + - - +
181A GLU* 3.6 46.9 - - + +
184A LYS* 5.7 4.9 - - + -
185A LEU* 4.8 6.1 - - + +
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 1.3 75.1 - - - +
81A GLU* 1.3 62.1 + - - +
83A ALA* 3.7 4.0 - - - +
84A LYS* 3.3 22.2 + - - +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.5 1.6 - - - +
80A GLY* 1.3 71.6 - - - +
82A LEU* 1.3 66.3 + - + +
84A LYS* 3.4 4.6 + - - +
85A HIS* 2.6 47.4 + - + +
181A GLU* 2.9 31.9 - - - +
700C ARG* 3.2 40.8 + - + +
701C SER* 4.8 3.5 - - - -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.7 24.4 - - + +
79A PRO* 3.6 28.9 + - + -
80A GLY 3.4 0.2 - - - -
81A GLU* 1.3 73.4 - - - +
83A ALA* 1.3 59.1 + - - +
85A HIS* 3.4 7.1 + - - +
86A ALA* 2.9 30.0 + - - +
146A TYR* 4.5 5.1 - - + -
147A LEU* 4.9 5.2 - - + -
150A GLU* 3.8 26.9 - - - +
181A GLU* 2.8 37.5 - - + +
182A LEU* 4.2 17.3 - - + -
185A LEU* 5.3 1.8 - - + -
700C ARG* 3.2 17.7 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 5.3 0.4 - - - +
75A ARG* 4.0 27.5 - - + +
78A LEU* 3.7 16.1 - - - +
79A PRO 2.8 22.9 + - - +
80A GLY* 3.7 5.6 - - - +
81A GLU 3.3 0.2 - - - -
82A LEU* 1.3 78.0 - - - +
84A LYS* 1.3 63.1 + - - +
86A ALA* 3.3 6.0 + - - +
87A VAL* 3.2 27.8 + - - +
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY 3.3 11.5 + - - +
81A GLU* 3.7 10.1 - - - +
82A LEU 3.3 0.2 - - - -
83A ALA* 1.3 78.0 - - - +
85A HIS* 1.3 72.5 + - + +
87A VAL* 3.3 20.6 + - - +
88A SER* 3.7 7.8 + - - -
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Residues in contact with HIS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 2.6 38.4 + - + +
82A LEU 3.8 4.7 - - - +
83A ALA 3.3 0.4 - - - -
84A LYS* 1.3 83.2 - - + +
86A ALA* 1.3 64.7 + - - +
88A SER* 3.2 9.3 + - - +
89A GLU* 2.9 36.8 + - - +
146A TYR* 3.6 13.6 + - - +
698C LEU* 3.6 20.2 - - + +
699C LEU 3.6 17.0 + - - -
700C ARG* 3.2 30.3 + - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.6 28.3 - - + -
78A LEU* 3.9 11.2 - - + -
82A LEU 2.9 17.5 + - - +
83A ALA 3.5 7.0 - - - +
85A HIS* 1.3 76.5 - - - +
87A VAL* 1.3 61.7 + - - +
89A GLU* 3.2 19.5 + - - +
90A GLY* 3.1 19.6 + - - -
139A TYR* 3.6 8.2 + - - -
143A VAL* 4.5 7.2 - - + +
146A TYR* 5.4 0.2 - - + -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 5.7 7.6 - - + +
74A VAL* 6.2 0.7 - - + -
75A ARG* 4.6 21.5 - - + -
83A ALA 3.2 17.0 + - - +
84A LYS* 3.5 10.5 - - - +
85A HIS 3.2 0.2 - - - -
86A ALA* 1.3 78.0 - - + +
88A SER* 1.3 56.8 + - - +
91A THR* 2.5 46.7 + - - +
139A TYR* 3.4 13.9 + - - +
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS 3.7 7.4 + - - -
85A HIS* 3.2 12.2 + - - -
87A VAL* 1.3 79.0 - - - +
89A GLU* 1.3 57.4 + - - +
91A THR* 4.5 3.4 - - - -
92A LYS* 3.0 43.8 + - - +
698C LEU* 5.0 8.5 - - - -
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A HIS 2.9 24.2 - - - +
86A ALA* 3.2 14.6 + - - +
88A SER* 1.3 77.3 - - - +
90A GLY* 1.3 61.2 + - - +
92A LYS* 4.1 2.9 - - - +
93A ALA* 3.2 16.6 + - - +
142A ALA* 3.3 27.7 - - + +
143A VAL* 4.1 6.2 - - - +
146A TYR* 2.8 64.6 - - + +
698C LEU* 3.3 15.0 - - + +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA 3.1 7.5 + - - -
89A GLU* 1.3 77.0 - - - +
91A THR* 1.3 65.5 + - - +
93A ALA* 3.3 2.9 + - - +
94A VAL* 3.1 27.5 + - - +
139A TYR* 3.4 36.4 - - - -
142A ALA* 3.9 11.8 - - - +
143A VAL* 5.1 0.6 - - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 4.2 14.1 + - - +
87A VAL* 2.5 36.0 + - - +
88A SER* 4.0 4.0 - - - -
90A GLY* 1.3 75.7 - - - +
92A LYS* 1.3 59.6 + - + +
94A VAL* 3.2 8.8 + - - +
95A THR* 2.8 36.7 + - - +
139A TYR* 3.7 3.4 - - - -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.0 33.4 + - - +
89A GLU* 4.1 3.8 - - - +
91A THR* 1.3 75.7 - - + +
93A ALA* 1.3 56.3 + - - +
95A THR* 3.2 13.7 + - + +
96A LYS* 2.8 36.8 + - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU 3.2 20.1 + - - +
90A GLY 3.5 5.6 - - - +
91A THR 3.2 0.2 - - - -
92A LYS* 1.3 76.2 - - - +
94A VAL* 1.3 57.5 + - - +
96A LYS* 3.5 6.4 + - - +
97A TYR* 3.0 28.2 + - - +
110A ALA 4.3 6.5 - - - +
112A LEU* 4.2 10.5 - - + -
138A VAL* 3.5 23.8 - - + +
142A ALA* 3.8 17.5 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 4.6 7.9 - - - +
90A GLY 3.1 16.5 + - - +
91A THR* 3.5 8.7 - - - +
93A ALA* 1.3 75.0 - - - +
95A THR* 1.3 59.2 + - - +
97A TYR* 3.2 7.5 + - + +
98A THR* 2.9 44.7 + - + +
135A GLY* 3.7 35.0 - - - +
138A VAL* 4.4 4.9 - - + -
139A TYR* 4.5 9.0 - - + -
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 2.8 24.0 + - - +
92A LYS* 3.5 19.4 - - + +
94A VAL* 1.3 77.4 - - - +
96A LYS* 1.3 50.9 + - - +
98A THR* 2.5 22.6 + - - +
99A SER* 2.7 28.2 + - - -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS 2.8 21.0 + - - +
93A ALA* 3.7 6.1 - - - +
95A THR* 1.3 72.4 - - - +
97A TYR* 1.3 62.7 + - - +
99A SER* 3.5 7.7 - - - -
100A SER* 3.0 32.2 + - - +
108A SER 6.0 0.4 - - - -
109A ARG 3.8 4.3 - - - +
110A ALA 3.3 20.0 - - - +
111A GLY* 4.0 21.4 + - - -
695C ASP* 5.2 9.7 + - - -
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA 3.0 15.0 + - - +
94A VAL* 3.4 12.6 - - + +
96A LYS* 1.3 78.5 - - - +
98A THR* 1.3 70.3 + - + +
100A SER 3.6 1.9 + - - -
106A ARG* 4.0 30.8 + - + +
109A ARG* 2.9 91.8 + - + +
110A ALA* 4.0 14.6 - - + +
134A ALA* 4.6 20.9 - - + +
135A GLY* 6.4 2.0 - - - -
138A VAL* 4.1 16.4 - - + -
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A VAL* 2.9 28.5 + - + +
95A THR* 2.5 30.1 + - - +
97A TYR* 1.3 84.3 - - + +
99A SER* 1.3 60.5 + - - +
100A SER 3.6 6.8 - - - +
109A ARG* 4.4 6.3 + - - +
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 2.7 24.5 + - - -
96A LYS* 3.2 11.6 + - - -
98A THR* 1.3 70.8 + - - +
100A SER* 1.4 65.2 + - - +
101A ALA* 3.4 4.9 + - - +
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS* 3.0 14.5 + - - +
98A THR 3.4 4.2 - - - +
99A SER* 1.4 77.5 - - - +
101A ALA* 1.3 60.2 + - - +
102A SER 5.2 1.6 - - - -
103A ALA* 4.7 6.3 - - - -
108A SER 5.0 1.0 + - - -
109A ARG* 3.3 67.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il