Contacts of the strand formed by residues 102 - 113 (chain A) in PDB entry 4FYT
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 VAL 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PRO* 3.9 0.2 - - - +
92A TYR* 2.8 52.2 + - + +
94A THR 5.5 0.2 + - - -
96A ASN* 3.7 27.8 - - + +
100A LEU* 3.9 8.2 + - + +
101A TYR* 1.3 79.9 - - - +
103A PHE* 1.3 62.3 + - - +
104A LYS* 4.8 5.2 - - - -
183A GLU* 3.4 29.4 - - - +
184A GLY 3.3 7.9 - - - +
186A LEU* 3.8 7.4 - - - +
1001A NAG 3.9 19.3 - - + +
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.0 14.6 - - + -
90A ARG 3.2 13.5 - - - +
91A PRO* 3.9 7.0 - - + -
92A TYR* 4.5 0.4 - - - -
102A VAL* 1.3 74.4 - - - +
104A LYS* 1.3 65.4 + - - +
127A LEU* 3.9 7.2 - - + -
182A PHE* 4.4 4.0 - + - -
183A GLU* 3.3 5.9 - - - +
184A GLY* 2.9 65.9 + - - +
185A GLU 3.5 17.0 - - - -
186A LEU* 4.0 7.0 - - + -
193A PHE* 3.7 40.4 - + + -
219A LYS* 3.5 24.7 - - - -
220A SER* 3.5 24.9 - - - -
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Residues in contact with LYS 104 (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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88A THR* 5.7 0.2 - - - +
89A LEU* 3.6 0.5 - - - -
90A ARG* 2.8 39.3 + - + +
92A TYR* 3.6 38.0 + - + +
102A VAL* 4.8 4.3 - - - -
103A PHE* 1.3 81.1 - - - +
105A GLY* 1.3 59.9 + - - +
182A PHE 3.6 4.9 - - - +
183A GLU* 4.0 33.9 - - + +
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Residues in contact with GLY 105 (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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88A THR* 3.0 13.9 - - - -
89A LEU* 3.9 2.0 - - - -
104A LYS* 1.3 76.6 - - - +
106A SER* 1.3 60.6 + - - -
181A GLU* 3.5 4.2 - - - +
182A PHE* 2.8 52.1 + - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.5 4.3 - - - +
88A THR* 2.9 48.1 + - - +
105A GLY* 1.3 75.1 - - - -
107A SER* 1.3 64.6 + - - +
180A SER 3.2 13.9 - - - -
181A GLU* 4.4 11.2 - - - -
182A PHE* 3.5 4.6 - - - -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.3 5.9 - - - -
86A ARG* 2.9 19.4 + - - -
87A VAL* 3.6 15.1 - - - +
106A SER* 1.3 76.9 - - - +
108A THR* 1.3 68.3 + - - +
109A VAL* 4.3 1.3 + - - +
178A MET 3.7 0.6 - - - +
179A ASP* 3.3 4.2 - - - +
180A SER* 2.8 45.8 + - - +
182A PHE* 3.7 8.9 - - - -
221A PHE* 4.2 11.4 - - - -
222A PRO* 4.7 4.2 + - - -
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Residues in contact with THR 108 (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 TYR* 3.3 3.1 - - - -
86A ARG* 2.9 67.7 + - - +
107A SER* 1.3 77.8 + - - +
109A VAL* 1.3 61.9 + - - +
140A ARG* 3.7 13.0 - - - +
177A GLU* 3.8 23.6 - - + +
178A MET 3.2 4.7 - - - +
179A ASP* 2.6 28.5 + - - +
1C NAG 3.8 3.6 - - + +
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Residues in contact with VAL 109 (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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82A PRO* 4.1 3.8 - - + -
84A SER 3.5 4.9 - - - +
85A TYR* 3.5 39.9 - - + -
107A SER* 4.3 1.3 + - - +
108A THR* 1.3 75.3 - - - +
110A ARG* 1.3 72.6 + - - +
111A PHE* 3.8 8.6 - - + -
122A ILE* 4.2 10.3 - - + -
177A GLU* 3.2 2.8 - - - -
178A MET* 3.0 61.5 + - + +
222A PRO 5.4 1.6 - - - +
224A PHE* 4.0 15.3 - - + -
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Residues in contact with ARG 110 (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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82A PRO* 3.7 1.7 - - - +
83A ASP* 2.8 26.3 + - + +
84A SER* 2.8 30.1 + - - +
108A THR 4.1 0.6 - - - -
109A VAL* 1.3 73.2 - - - +
111A PHE* 1.3 63.3 + - - +
142A VAL* 3.5 28.2 - - + +
175A GLN* 3.8 31.9 + - - +
176A TYR 3.3 10.8 - - - +
177A GLU* 2.7 36.8 + - + +
1C NAG 4.6 12.0 + - + +
2C NAG 2.7 33.9 + - - -
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Residues in contact with PHE 111 (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 LEU* 4.0 38.6 - - + -
81A LYS 3.5 15.3 - - - +
82A PRO* 3.7 9.0 - - + -
83A ASP* 3.4 7.6 - - - -
109A VAL* 3.8 18.2 - - + -
110A ARG* 1.3 75.3 - - - +
112A THR* 1.3 63.7 + - - +
113A CYS 4.6 0.2 - - - -
120A ILE* 3.7 30.1 - - + -
139A LEU* 4.1 1.3 - - + -
170A LEU* 4.1 7.6 - - + -
175A GLN* 3.2 5.2 - - - +
176A TYR* 2.9 65.9 + + + -
177A GLU 4.5 0.4 - - - -
178A MET* 4.1 23.8 - - + -
224A PHE* 4.2 13.0 - + + -
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Residues in contact with THR 112 (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 LEU* 3.5 2.4 - - - +
81A LYS* 2.8 37.5 + - - -
83A ASP* 2.8 26.8 + - - -
111A PHE* 1.3 75.2 - - - +
113A CYS* 1.3 74.5 + - - +
114A LYS* 3.5 23.1 + - + +
173A ASP* 4.3 12.6 - - - +
174A SER 3.5 10.3 - - - +
175A GLN* 3.4 13.2 + - + +
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Residues in contact with CYS 113 (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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79A THR 3.7 4.9 - - - -
80A LEU* 3.9 12.3 - - + +
111A PHE* 4.2 2.2 + - - -
112A THR* 1.3 73.8 - - - +
114A LYS* 1.3 54.8 + - - +
115A GLU 3.1 33.4 - - - -
116A ALA* 3.9 2.5 - - - -
117A THR 4.5 0.9 - - - -
170A LEU* 3.9 15.7 - - + -
171A VAL 3.3 30.5 - - - +
172A LYS 4.0 0.2 - - - -
173A ASP* 2.6 34.3 + - - +
174A SER 2.8 13.3 + - - +
176A TYR* 3.9 12.8 - - + -
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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
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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