Contacts of the strand formed by residues 102 - 117 (chain A) in PDB entry 2EA3
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 GLY 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.7 28.5 - - - -
96A ARG* 3.3 13.9 + - - +
97A SER* 3.5 0.4 - - - -
98A GLY 2.9 36.1 + - - -
99A SER 4.7 0.6 - - - -
100A THR 3.7 0.8 - - - -
101A THR* 1.3 79.0 - - - +
103A TRP* 1.3 58.4 + - - -
104A HIS* 3.9 0.4 + - - -
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Residues in contact with TRP 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A VAL* 4.2 13.5 - - + -
73A ASN 3.8 12.1 - - - -
74A ASN* 3.3 41.5 - - + +
75A TYR* 4.2 4.3 - - + +
80A VAL* 3.8 29.8 - - + -
95A CYS* 3.3 30.7 - - + -
96A ARG 3.3 19.7 - - - -
97A SER* 4.0 4.5 - - - -
101A THR 3.7 1.8 + - - -
102A GLY* 1.3 69.6 - - - -
104A HIS* 1.3 72.2 + - - +
105A CYS* 3.5 17.5 - - - -
142A LEU* 4.1 13.9 - - + -
144A GLY 5.8 0.4 - - - -
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Residues in contact with HIS 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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96A ARG* 2.8 56.9 + - - +
101A THR* 2.8 37.6 + - - -
103A TRP* 1.3 88.9 + - - +
105A CYS* 1.3 64.9 + - - +
130A VAL* 3.6 11.0 - - + +
131A CYS* 3.6 20.6 - - - +
158A CYS* 4.0 17.9 - - + +
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Residues in contact with CYS 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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93A ALA* 6.3 1.1 - - + -
94A VAL 3.2 6.3 - - - +
95A CYS* 2.0 47.6 - - - -
103A TRP* 3.5 17.9 - - - -
104A HIS* 1.3 77.0 - - - +
106A GLY* 1.3 60.0 + - - +
129A THR 4.6 1.9 - - - +
130A VAL* 3.8 12.4 - - - -
131A CYS 5.2 0.3 + - - -
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Residues in contact with GLY 106 (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* 3.4 5.2 - - - +
94A VAL* 2.8 29.4 + - - +
105A CYS* 1.3 78.0 - - - +
107A THR* 1.3 69.5 + - - +
129A THR* 3.4 13.0 - - - -
130A VAL* 3.5 9.5 - - - +
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Residues in contact with THR 107 (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 GLY* 4.2 14.8 - - - +
92A SER 3.2 12.3 - - - +
93A ALA* 4.5 6.3 - - + -
94A VAL* 4.1 6.7 - - - +
106A GLY* 1.3 80.4 - - - +
108A ILE* 1.3 64.7 + - - +
109A THR* 3.5 13.9 + - - +
128A THR* 3.2 3.1 - - - -
129A THR* 3.0 35.7 + - - +
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Residues in contact with ILE 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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88A ALA* 3.9 25.8 - - + +
89A PRO 3.9 6.7 - - - +
90A VAL* 3.7 15.6 - - - +
91A GLY* 2.7 34.5 + - - +
92A SER* 3.0 16.4 + - - +
94A VAL* 3.7 33.0 - - + -
107A THR* 1.3 72.9 + - - +
109A THR* 1.3 62.8 + - - +
110A ALA 3.7 20.2 - - - +
111A LEU* 3.9 10.3 - - + -
126A ILE* 3.9 24.0 - - + -
127A ARG 3.6 4.0 - - - -
128A THR* 4.2 1.8 - - + -
141A LEU* 5.3 0.7 - - + -
148A GLN* 4.5 7.6 - - + +
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Residues in contact with THR 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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90A VAL* 3.8 14.5 - - - +
107A THR* 3.9 10.5 - - - +
108A ILE* 1.3 77.1 - - - +
110A ALA* 1.3 59.3 + - - +
127A ARG* 2.8 42.7 + - - +
128A THR* 4.1 1.9 + - - -
129A THR* 3.8 29.2 - - + +
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Residues in contact with ALA 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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90A VAL* 4.1 7.4 - - - -
108A ILE* 3.7 2.6 - - - +
109A THR* 1.3 81.1 + - - +
111A LEU* 1.3 72.1 + - - +
113A SER* 3.6 19.7 - - - +
126A ILE* 3.6 3.1 - - - -
127A ARG* 2.8 38.3 + - + +
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Residues in contact with LEU 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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88A ALA 4.6 14.4 - - - +
89A PRO* 5.2 2.0 - - + -
90A VAL* 3.7 26.7 - - + +
108A ILE* 3.9 17.7 - - + -
110A ALA* 1.3 82.9 - - - +
112A ASN* 1.3 73.4 + - + +
113A SER* 3.2 6.1 + - - -
125A LEU 3.9 2.7 - - - -
126A ILE* 4.1 20.2 - - + -
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Residues in contact with ASN 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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111A LEU* 1.3 77.5 - - + +
113A SER* 1.3 62.8 + - - +
114A SER* 5.0 1.9 + - - -
123A ARG* 5.2 1.0 - - - +
124A GLY* 2.9 33.2 + - - -
125A LEU 3.1 8.3 + - - -
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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
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110A ALA* 3.6 15.1 - - - +
111A LEU 4.2 0.4 + - - -
112A ASN* 1.3 74.2 - - - +
114A SER* 1.3 61.7 + - - +
123A ARG 3.6 0.7 - - - -
124A GLY 3.2 7.8 + - - -
125A LEU* 2.8 39.6 + - - +
127A ARG* 3.5 21.5 - - - +
165A PHE* 3.8 25.1 - - - -
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Residues in contact with SER 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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112A ASN 4.1 2.1 + - - -
113A SER* 1.3 75.6 - - - +
115A VAL* 1.3 70.1 + - - +
121A THR* 4.4 9.0 - - - -
122A VAL 3.2 7.4 - - - -
123A ARG* 3.2 29.0 + - - +
124A GLY 4.8 0.2 + - - -
165A PHE* 4.7 2.3 - - - -
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Residues in contact with VAL 115 (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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114A SER* 1.3 80.6 - - - +
116A THR* 1.3 64.2 + - - +
117A TYR* 3.5 41.0 + - + +
121A THR* 3.2 5.3 - - - +
122A VAL* 2.9 33.2 + - + +
125A LEU* 3.7 14.3 - - + +
165A PHE* 3.5 47.6 - - + -
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Residues in contact with THR 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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115A VAL* 1.3 75.7 - - - +
117A TYR* 1.3 73.3 + - - +
118A PRO* 4.8 0.5 - - - +
120A GLY* 3.8 7.4 - - - -
121A THR* 3.3 24.6 + - - +
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Residues in contact with TYR 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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32A HIS* 5.7 0.9 - + - -
52A PHE* 3.8 15.9 - + + -
56A ASP* 4.8 0.2 - - - -
115A VAL* 3.5 29.7 - - + +
116A THR* 1.3 85.8 - - - +
118A PRO* 1.4 79.3 - - + +
119A GLU* 3.6 14.4 - - - +
120A GLY* 2.9 20.7 + - - +
122A VAL* 3.6 26.9 - - + -
125A LEU* 4.6 1.0 - - - +
152A SER* 2.6 33.2 + - - -
153A GLY* 3.0 31.4 + - - -
154A GLY* 4.4 7.4 - - - -
165A PHE* 4.7 0.7 - - - +
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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
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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