Contacts of the strand formed by residues 103 - 115 (chain S) in PDB entry 1H2I
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 PHE 103 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96S VAL* 4.1 15.5 - - + -
97S ASP 3.2 11.4 - - - -
98S LEU* 3.8 35.0 - - + -
101S GLY 4.8 1.6 - - - -
102S LYS* 1.3 73.1 - - - +
104S TYR* 1.3 64.8 + - - +
105S VAL* 4.1 4.5 - - + -
129S SER 3.3 7.0 - - - +
130S GLU* 3.6 0.2 - - - -
131S GLY 3.0 22.5 + - - -
132S LEU 2.8 11.4 + - - -
133S LYS* 3.2 32.1 - - - -
134S SER 3.8 0.9 - - - -
135S LYS* 3.5 50.3 - - + -
138S SER* 3.7 21.1 + - - +
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Residues in contact with TYR 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S PHE* 3.2 17.9 - - + -
96S VAL* 3.6 0.2 - - - -
97S ASP* 2.6 49.3 + - + +
99S ASN* 4.0 24.2 - - + +
100S ASN* 3.4 24.8 + - - -
102S LYS* 3.4 34.4 + - + +
103S PHE* 1.3 72.9 - - - +
105S VAL* 1.3 61.4 + - - +
129S SER 3.4 2.5 - - - -
130S GLU* 3.6 33.2 - - + +
131S GLY* 3.7 17.8 - - - -
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Residues in contact with VAL 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136R ALA* 5.0 0.2 - - - -
93S VAL* 4.8 0.4 - - + -
95S PHE* 3.4 14.1 - - - +
96S VAL* 4.2 20.6 - - + -
103S PHE* 4.5 1.8 - - + -
104S TYR* 1.3 81.8 - - - +
106S GLY* 1.3 62.4 + - - +
107S VAL* 4.0 7.0 - - + -
127S GLY 4.4 0.2 - - - -
128S VAL* 3.4 10.2 - - - +
129S SER* 2.8 37.3 + - - +
130S GLU* 4.9 1.0 - - - +
135S LYS* 6.3 0.4 - - + -
138S SER* 3.8 27.6 - - - +
139S LEU* 3.7 26.2 - - + +
142S ALA* 3.8 19.5 - - + -
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Residues in contact with GLY 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136R ALA* 4.6 0.9 - - - -
93S VAL 3.8 0.2 - - - -
94S ASP* 2.9 27.4 + - - +
95S PHE* 3.2 22.0 + - - +
105S VAL* 1.3 75.8 - - - +
107S VAL* 1.3 64.1 + - - +
126S TYR* 3.3 24.9 - - - -
127S GLY 3.5 4.3 - - - -
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Residues in contact with VAL 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S GLN* 3.7 35.9 - - + +
92S ASN 3.6 11.7 - - - +
93S VAL* 3.8 23.6 - - + -
94S ASP 4.4 0.2 - - - +
105S VAL* 4.0 8.1 - - + -
106S GLY* 1.3 80.2 - - - +
108S CYS* 1.3 62.7 + - - +
126S TYR* 3.2 10.2 - - - -
127S GLY 2.7 37.1 + - - -
139S LEU* 4.7 0.9 - - + -
142S ALA* 3.7 31.6 - - + +
143S ARG* 4.1 7.9 - - + +
146S ALA* 3.6 5.3 - - + +
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Residues in contact with CYS 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143R ARG* 3.3 37.7 - - - -
91S GLN* 3.4 5.0 - - - +
92S ASN* 2.8 50.2 + - - -
94S ASP* 4.7 0.2 + - - -
107S VAL* 1.3 74.8 - - - +
109S ALA* 1.3 60.5 + - - +
110S PHE* 3.8 18.6 - - - -
124S VAL* 4.5 5.8 - - + -
125S GLY 3.3 6.7 - - - +
126S TYR* 3.6 20.4 - - + -
146S ALA* 4.0 2.7 - - - -
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Residues in contact with ALA 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S ILE* 5.1 2.2 - - + -
90S GLN 3.5 7.2 - - - +
91S GLN* 4.0 11.2 - - + +
108S CYS* 1.3 73.5 - - - +
110S PHE* 1.3 64.1 + - - +
111S VAL* 3.8 7.0 + - + +
123S ASP 3.7 0.7 - - - +
124S VAL* 3.2 4.7 - - - -
125S GLY 2.8 34.8 + - - -
146S ALA* 3.7 31.6 - - + +
147S VAL* 3.8 14.4 - - + +
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Residues in contact with PHE 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88R ILE* 3.9 31.2 - - + -
91R GLN* 3.3 44.2 - - + -
143R ARG* 4.5 4.7 - - - -
88S ILE* 3.5 4.9 - - - +
89S THR* 2.8 47.8 + - - +
90S GLN* 2.7 41.9 + - + +
108S CYS* 3.8 23.3 - - - -
109S ALA* 1.3 73.2 - - - +
111S VAL* 1.3 58.0 + - - +
122S GLU* 3.8 5.6 - - - +
123S ASP 3.5 2.7 - - - +
124S VAL* 3.1 23.6 - - + -
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Residues in contact with VAL 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S HIS* 4.0 25.1 - - + -
87S SER 3.4 10.5 - - - +
88S ILE* 4.6 9.4 - - + -
109S ALA* 4.4 6.5 - - + -
110S PHE* 1.3 76.7 - - - +
112S ARG* 1.3 63.2 + - - +
113S VAL 4.0 0.2 - - - -
122S GLU* 3.2 5.9 - - - -
123S ASP 3.0 31.3 + - - -
147S VAL* 3.6 31.0 - - + +
150S GLY* 3.7 17.0 - - - -
151S LEU* 3.7 22.7 - - + +
154S ALA* 3.8 6.7 - - + +
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Residues in contact with ARG 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R SER* 5.2 5.3 - - - -
86S HIS* 3.0 4.2 - - - -
87S SER* 2.8 44.9 + - - +
89S THR* 4.0 24.0 - - + +
110S PHE 4.2 0.6 + - - -
111S VAL* 1.3 72.3 - - - +
113S VAL* 1.3 65.0 + - - +
114S GLN* 3.0 35.0 + - - +
118S GLY 4.8 0.6 + - - -
120S TYR* 3.6 46.8 - - + +
121S HIS 3.7 5.6 - - - +
122S GLU* 4.0 22.4 - - + -
120T TYR* 4.9 6.4 + - - -
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Residues in contact with VAL 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84S TRP* 4.1 11.9 - - + -
85S ALA 3.1 12.6 - - - +
86S HIS* 4.0 7.4 - - + +
111S VAL 4.0 0.4 - - - -
112S ARG* 1.3 76.1 - - - +
114S GLN* 1.3 66.7 + - - +
120S TYR* 3.2 6.3 - - - +
121S HIS 2.9 42.6 + - - +
151S LEU* 4.7 3.1 - - + -
154S ALA* 3.3 34.5 - - + +
155S LEU* 3.5 27.1 - - + +
158S PHE* 4.0 17.5 - - + -
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Residues in contact with GLN 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S PHE* 3.3 16.1 - - + -
27S GLY* 3.5 17.4 - - - -
84S TRP* 3.1 2.8 - - - +
85S ALA 2.7 39.8 + - - +
112S ARG* 3.0 28.7 + - - +
113S VAL* 1.3 75.6 - - - +
115S LEU* 1.3 77.3 + - - +
118S GLY* 3.5 25.1 - - - +
119S SER 3.2 13.2 - - - +
120S TYR* 4.3 0.2 - - + -
158S PHE* 5.4 0.2 - - - -
120T TYR* 3.3 22.8 + - - +
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Residues in contact with LEU 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R TYR* 4.1 19.7 - - + -
26S PHE* 3.4 4.4 - - - -
31S TYR* 3.6 20.0 - - + +
79S PHE* 4.1 15.0 - - + -
83S GLY 3.2 9.2 - - - +
84S TRP* 4.0 11.9 - - + -
113S VAL* 4.9 0.7 - - + -
114S GLN* 1.3 89.2 + - - +
116S LYS* 1.3 54.3 + - - +
117S ASP* 2.8 8.4 + - + -
118S GLY 2.8 22.7 + - - -
119S SER* 2.9 33.9 + - - +
158S PHE* 3.3 43.5 - - + -
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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