Contacts of the strand formed by residues 103 - 115 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96P VAL* 4.2 15.5 - - + -
97P ASP 3.1 12.8 - - - -
98P LEU* 3.7 33.7 - - + -
101P GLY 4.7 1.3 - - - -
102P LYS* 1.3 72.1 - - - +
104P TYR* 1.3 64.5 - - - +
105P VAL* 4.1 4.9 - - + -
129P SER 3.3 7.6 - - - +
130P GLU 3.7 0.2 - - - -
131P GLY 3.0 22.9 + - - -
132P LEU 2.8 12.1 + - - -
133P LYS* 3.2 32.8 - - - -
134P SER 3.8 0.4 - - - -
135P LYS* 3.6 50.3 - - + -
138P SER* 3.8 20.3 + - - +
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Residues in contact with TYR 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P PHE* 3.2 17.7 - - + -
96P VAL* 3.6 0.2 - - - -
97P ASP* 2.6 53.1 + - + +
99P ASN* 3.9 25.6 - - + +
100P ASN* 3.3 25.6 + - - -
102P LYS* 3.5 29.3 - - - +
103P PHE* 1.3 72.9 - - - +
105P VAL* 1.3 60.9 + - - +
129P SER 3.4 2.5 - - - -
130P GLU* 3.6 33.4 - - + +
131P GLY* 3.8 17.5 - - - -
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Residues in contact with VAL 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O ALA* 4.7 0.2 - - - -
95P PHE* 3.4 15.4 - - - +
96P VAL* 4.2 20.4 - - + -
103P PHE* 4.4 2.0 - - + -
104P TYR* 1.3 83.5 - - - +
106P GLY* 1.3 61.4 + - - +
107P VAL* 4.1 6.3 - - + -
127P GLY 3.7 0.4 - - - +
128P VAL* 3.4 10.6 - - - +
129P SER* 2.8 37.1 + - - +
130P GLU* 4.9 1.0 - - - +
135P LYS* 5.5 0.4 - - - +
138P SER* 3.8 26.5 - - - +
139P LEU* 3.7 27.8 - - + +
142P ALA* 3.9 19.2 - - + +
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Residues in contact with GLY 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O ALA* 4.4 0.4 - - - -
93P VAL 3.7 0.2 - - - -
94P ASP* 2.8 27.5 + - - +
95P PHE* 3.3 22.0 + - - +
105P VAL* 1.3 76.0 - - - +
107P VAL* 1.3 64.9 + - - +
126P TYR* 3.4 24.9 - - - -
127P GLY 3.6 4.3 - - - -
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Residues in contact with VAL 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P GLN* 3.7 36.6 - - + +
92P ASN 3.6 10.1 - - - +
93P VAL* 3.8 23.6 - - + -
94P ASP 4.4 0.2 - - - +
105P VAL* 4.1 8.3 - - + -
106P GLY* 1.3 80.0 - - - +
108P CYS* 1.3 63.7 + - - +
126P TYR* 3.3 9.1 - - - -
127P GLY 2.6 37.5 + - - -
139P LEU* 4.7 0.7 - - + -
142P ALA* 3.7 27.6 - - + +
143P ARG* 4.0 11.0 - - + +
146P ALA* 3.5 5.1 - - + +
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Residues in contact with CYS 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143O ARG* 3.4 38.4 - - - -
91P GLN* 3.3 6.2 - - - +
92P ASN* 2.8 51.1 + - - -
94P ASP* 4.6 0.4 + - - -
107P VAL* 1.3 75.5 - - - +
109P ALA* 1.3 60.4 + - - +
110P PHE* 3.8 17.5 - - - -
124P VAL* 4.5 5.8 - - + -
125P GLY 3.3 11.0 - - - +
126P TYR* 3.7 16.5 - - + -
146P ALA* 4.1 1.8 - - - -
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Residues in contact with ALA 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88P ILE* 5.0 2.0 - - + -
90P GLN 3.3 8.7 - - - +
91P GLN* 4.0 11.0 - - + +
108P CYS* 1.3 74.7 - - - +
110P PHE* 1.3 65.1 + - - +
111P VAL* 3.9 6.9 + - + +
123P ASP 3.7 0.3 - - - +
124P VAL* 3.2 5.1 - - - -
125P GLY* 2.8 30.3 + - - -
146P ALA* 3.7 30.3 - - + +
147P VAL* 3.8 14.1 - - + +
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Residues in contact with PHE 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ILE* 3.8 31.6 - - + -
91O GLN* 3.2 44.9 - - + -
143O ARG* 4.6 4.3 - - - -
88P ILE* 3.5 5.0 - - - -
89P THR* 2.8 44.9 + - - +
90P GLN* 2.7 41.5 + - + +
108P CYS* 3.8 24.0 - - - -
109P ALA* 1.3 73.2 - - - +
111P VAL* 1.3 60.3 + - - +
122P GLU* 3.7 4.9 - - - +
123P ASP 3.5 3.6 - - - +
124P VAL* 3.2 22.9 - - + -
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Residues in contact with VAL 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P HIS* 3.9 26.7 - - + -
87P SER 3.3 11.9 - - - +
88P ILE* 4.6 4.7 - - + -
109P ALA* 4.5 6.7 - - + -
110P PHE* 1.3 77.8 - - - +
112P ARG* 1.3 64.1 + - - +
113P VAL 4.9 0.2 - - - +
122P GLU* 3.3 5.8 - - - +
123P ASP 3.1 28.1 + - - -
147P VAL* 3.7 36.1 - - + +
150P GLY* 3.9 16.4 - - - +
151P LEU* 3.8 22.0 - - + +
154P ALA* 3.8 7.0 - - + +
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Residues in contact with ARG 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O SER* 5.1 4.8 - - - -
86P HIS* 3.1 3.9 - - - +
87P SER* 2.8 40.9 + - - +
89P THR* 3.9 23.7 - - + +
110P PHE 4.2 0.8 + - - -
111P VAL* 1.3 73.9 - - - +
113P VAL* 1.3 63.9 + - - +
114P GLN* 2.9 35.2 + - - +
118P GLY 4.7 0.6 + - - -
120P TYR* 3.5 49.4 - - + +
121P HIS 3.6 5.6 - - - +
122P GLU* 3.9 24.0 - - + -
120Q TYR* 5.2 4.9 + - - -
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Residues in contact with VAL 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P TRP* 4.1 12.3 - - + -
85P ALA 3.1 16.6 - - - +
86P HIS* 4.0 7.0 - - + +
111P VAL* 3.9 0.4 + - + -
112P ARG* 1.3 75.1 - - - +
114P GLN* 1.3 64.7 + - - +
120P TYR* 3.2 6.1 - - - +
121P HIS 2.9 41.9 + - - +
151P LEU* 4.7 3.8 - - + -
154P ALA* 3.3 33.2 - - + +
155P LEU* 3.5 26.7 - - + +
158P PHE* 4.0 16.1 - - + -
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Residues in contact with GLN 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PHE* 3.3 16.0 - - + -
27P GLY* 3.5 17.0 - - - -
84P TRP* 3.2 3.5 - - - +
85P ALA 2.7 40.9 + - - +
112P ARG* 2.9 26.4 + - - +
113P VAL* 1.3 75.9 - - - +
115P LEU* 1.3 80.8 + - - +
118P GLY* 3.5 20.9 - - - +
119P SER 3.2 13.5 - - - +
120P TYR* 4.2 3.6 - - + +
120Q TYR* 3.3 21.6 + - - +
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Residues in contact with LEU 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O TYR* 4.1 16.2 - - + -
26P PHE* 3.5 6.8 - - - -
31P TYR* 3.6 14.4 - - + +
79P PHE* 4.1 20.6 - - + -
83P GLY 3.3 11.2 - - - +
84P TRP* 3.9 13.0 - - + -
113P VAL* 5.1 0.2 - - + -
114P GLN* 1.3 88.5 + - - +
116P LYS* 1.3 59.1 + - - +
117P ASP* 2.8 14.2 + - + -
118P GLY 2.9 10.2 + - - -
119P SER* 2.9 29.3 + - - +
158P PHE* 3.1 49.8 - - + -
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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