Contacts of the strand formed by residues 110 - 126 (chain A) in PDB entry 3D5K
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 ALA 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLN 3.9 0.2 - - - +
98A ARG* 3.5 2.1 - - - +
99A LEU* 2.8 37.6 + - + +
104A SER* 3.9 11.9 - - - -
105A THR* 5.6 1.3 - - - +
106A THR* 3.9 19.1 - - + +
108A SER 3.0 9.9 + - - +
109A PRO* 1.3 74.1 - - - +
111A ILE* 1.3 64.3 + - - +
112A SER 4.0 0.8 + - - -
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Residues in contact with ILE 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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96A ARG* 4.1 37.2 - - + +
97A GLN 3.4 8.7 - - - +
98A ARG* 3.9 21.1 - - + -
110A ALA* 1.3 78.4 - - - +
112A SER* 1.3 69.9 - - - +
113A SER* 4.1 2.3 + - - -
324B TRP* 3.7 29.2 - - + -
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Residues in contact with SER 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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95A THR* 4.7 1.1 - - - -
96A ARG* 3.6 3.3 - - - -
97A GLN* 2.9 53.1 + - - +
99A LEU* 3.8 16.8 - - - +
110A ALA 4.0 2.4 + - - -
111A ILE* 1.3 77.2 - - - +
113A SER* 1.3 63.0 + - - +
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 3.3 10.4 + - - -
96A ARG* 3.6 20.6 + - - +
111A ILE* 4.1 3.1 + - - -
112A SER* 1.3 77.1 - - - +
114A GLN* 1.3 62.3 + - - +
115A TYR* 3.1 18.9 + - - -
311A ARG* 3.1 40.3 + - - +
103C LEU* 4.0 13.2 - - - +
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Residues in contact with GLN 114 (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 SER 4.1 0.3 - - - +
94A GLY* 3.5 2.1 - - - -
95A THR* 2.9 54.4 + - + +
113A SER* 1.3 76.2 + - - +
115A TYR* 1.3 67.2 + - - +
309A MET* 3.4 30.0 - - + +
310A SER 3.7 5.4 - - - -
99C LEU* 4.5 8.5 - - - +
103C LEU* 3.7 23.5 - - + +
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 3.4 7.4 - - - -
94A GLY* 4.0 19.5 - - - -
95A THR 4.8 4.4 + - - -
96A ARG* 4.1 19.6 + - - +
113A SER* 3.1 25.5 + - - -
114A GLN* 1.3 77.0 - - - +
116A GLY* 1.3 59.4 + - - +
309A MET* 3.4 16.2 - - - +
310A SER 2.8 29.4 + - - +
311A ARG 3.3 19.3 - - - -
312A GLN* 3.6 15.3 - - - +
313A LEU* 3.6 41.1 - - + +
316A LEU* 4.1 17.3 - - + -
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Residues in contact with GLY 116 (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 ASP 3.5 2.5 - - - +
92A GLY* 3.3 3.1 - - - -
93A SER* 2.9 42.5 + - - +
115A TYR* 1.3 77.5 - - - +
117A VAL* 1.3 65.1 + - - +
118A THR* 4.1 2.0 - - - -
308A THR 3.2 13.0 - - - -
309A MET* 4.1 8.1 - - - -
316A LEU* 4.0 5.2 - - - +
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Residues in contact with VAL 117 (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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90A VAL* 4.3 20.2 - - + -
91A ASP 3.7 3.6 - - - +
92A GLY* 4.7 8.3 - - - -
116A GLY* 1.3 75.0 - - - +
118A THR* 1.3 63.0 + - - +
307A GLY* 3.5 2.1 - - - -
308A THR* 2.9 33.6 + - - +
316A LEU* 4.1 22.6 - - + +
317A PHE* 3.9 31.4 - - + -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.3 10.5 - - - +
91A ASP* 2.9 53.9 + - + +
116A GLY* 5.2 1.6 - - - -
117A VAL* 1.3 77.1 - - - +
119A LEU* 1.3 60.6 + - - +
120A GLY 4.8 0.9 - - - +
305A ASN* 2.9 39.7 + - + +
306A ALA 3.0 22.0 + - - -
307A GLY* 3.6 2.0 + - - -
308A THR 5.2 1.1 - - - -
309A MET* 6.2 2.0 - - - -
323A SER* 5.2 2.3 + - - -
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Residues in contact with LEU 119 (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 ILE* 4.0 20.0 - - + -
89A GLY 3.4 20.2 - - - +
90A VAL* 4.1 15.0 - - + -
118A THR* 1.3 73.4 + - - +
120A GLY* 1.3 59.0 + - - +
305A ASN* 3.4 4.0 - - - -
306A ALA* 2.8 34.8 + - - +
334B ILE* 4.2 12.6 - - + -
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Residues in contact with GLY 120 (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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87A ARG 3.5 1.0 - - - +
88A ILE* 3.5 9.7 - - - +
89A GLY 3.2 32.1 + - - +
91A ASP* 6.1 0.6 - - - +
118A THR* 4.2 2.4 - - - +
119A LEU* 1.3 75.1 - - - +
121A THR* 1.3 64.2 + - - -
122A THR* 4.5 2.4 + - - +
304A ALA 3.3 11.7 - - - -
305A ASN* 3.8 7.0 - - - +
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Residues in contact with THR 121 (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 PRO* 3.7 9.7 - - + +
87A ARG* 3.3 35.3 + - + +
88A ILE* 3.6 16.6 - - - +
120A GLY* 1.3 75.4 - - - -
122A THR* 1.3 67.7 + - - +
124A TRP* 3.7 29.4 - - + -
302A LEU 4.9 1.8 - - - -
303A THR* 3.4 8.1 - - - +
304A ALA* 2.9 35.0 + - - +
305A ASN* 4.8 0.7 - - - +
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Residues in contact with THR 122 (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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87A ARG* 4.6 2.8 + - - +
91A ASP* 5.6 6.7 - - - +
120A GLY 5.5 2.0 - - - +
121A THR* 1.3 79.9 - - - +
123A ALA* 1.3 75.9 + - - +
124A TRP* 3.5 1.0 + - - -
303A THR* 4.0 10.7 + - - -
331B ASN* 5.6 8.5 - - - +
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Residues in contact with ALA 123 (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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122A THR* 1.3 81.0 + - - +
124A TRP* 1.3 61.6 + - - +
125A GLU* 3.5 4.7 + - - +
301A SER* 3.7 17.5 - - - +
302A LEU 3.8 0.6 + - - -
303A THR* 3.1 17.6 + - - +
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Residues in contact with TRP 124 (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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83A ASP 5.0 4.0 - - - -
84A LEU 3.2 25.7 + - - -
85A PHE 4.2 2.9 - - - -
86A PRO* 3.5 49.2 - - + -
121A THR* 3.7 18.8 - - + -
122A THR 3.5 0.6 - - - -
123A ALA* 1.3 71.3 - - - +
125A GLU* 1.3 75.4 + - - +
126A LEU* 3.3 31.0 + - + -
301A SER* 3.3 3.9 - - - -
302A LEU* 2.8 75.6 + - + +
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Residues in contact with GLU 125 (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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83A ASP 5.8 0.2 - - - +
84A LEU 4.8 2.3 - - - +
123A ALA 3.5 6.0 + - - +
124A TRP* 1.3 85.4 + - - +
126A LEU* 1.3 69.7 + - - +
127A ASP* 3.4 5.9 + - - +
131A ARG* 3.0 47.1 + - - +
132A LEU* 3.8 30.6 - - + +
299A SER* 4.3 16.7 + - - +
300A ILE 3.4 13.5 - - - +
301A SER* 4.4 3.8 - - - +
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Residues in contact with LEU 126 (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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124A TRP* 3.3 41.9 + - + +
125A GLU* 1.3 71.3 - - - +
127A ASP* 1.3 54.2 + - - +
128A LEU* 2.8 22.0 + - + +
300A ILE* 2.9 51.1 + - + +
302A LEU* 4.6 24.0 - - + -
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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