Contacts of the strand formed by residues 103 - 115 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96H VAL* 4.3 12.8 - - + -
97H ASP 3.1 14.4 - - - -
98H LEU* 3.8 34.8 - - + -
101H GLY 4.9 1.3 - - - -
102H LYS* 1.3 72.1 - - - +
104H TYR* 1.3 64.5 + - - +
105H VAL* 4.5 3.8 - - + -
129H SER 3.3 7.8 - - - +
131H GLY* 3.0 21.8 + - - -
132H LEU 2.8 11.6 + - - -
133H LYS* 3.2 31.9 - - - -
134H SER 3.8 0.7 - - - -
135H LYS* 3.5 52.5 - - + -
138H SER* 3.7 20.7 + - - +
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Residues in contact with TYR 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H PHE* 3.1 19.1 - - + -
97H ASP* 2.6 48.9 + - + +
99H ASN* 4.0 25.4 - - + +
100H ASN* 3.3 25.1 + - - -
102H LYS* 3.5 33.9 + - + +
103H PHE* 1.3 72.4 - - - +
105H VAL* 1.3 61.0 + - - +
129H SER 3.5 2.5 - - - -
130H GLU* 3.5 39.9 - - + +
131H GLY* 3.8 9.7 - - - -
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Residues in contact with VAL 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ALA* 4.9 0.2 - - - -
93H VAL* 4.8 0.2 - - + -
95H PHE* 3.4 16.6 - - - +
96H VAL* 4.2 19.1 - - + -
103H PHE* 4.5 1.8 - - + -
104H TYR* 1.3 83.0 - - - +
106H GLY* 1.3 61.3 + - - +
107H VAL* 4.0 6.3 - - + -
127H GLY 3.7 0.5 - - - +
128H VAL* 3.4 10.2 - - - +
129H SER* 2.9 35.7 + - - +
130H GLU* 4.9 1.2 - - - +
135H LYS* 6.4 0.2 - - + -
138H SER* 3.9 25.8 - - - +
139H LEU* 3.6 26.7 - - + +
142H ALA* 3.8 19.5 - - + -
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Residues in contact with GLY 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ALA* 4.6 1.1 - - - -
93H VAL* 3.9 0.2 - - - -
94H ASP* 2.8 27.9 + - - +
95H PHE* 3.3 23.6 + - - +
105H VAL* 1.3 73.9 - - - +
107H VAL* 1.3 65.0 + - - +
126H TYR* 3.4 24.9 - - - -
127H GLY 3.6 4.3 - - - -
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Residues in contact with VAL 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H GLN* 3.7 39.9 - - + +
92H ASN 3.6 7.4 - - - +
93H VAL* 3.8 22.9 - - + -
94H ASP 4.3 0.2 - - - +
105H VAL* 4.0 9.0 - - + -
106H GLY* 1.3 81.4 - - - +
108H CYS* 1.3 63.5 + - - +
126H TYR* 3.3 8.8 - - - -
127H GLY 2.6 36.7 + - - -
139H LEU* 4.7 0.4 - - + -
142H ALA* 3.7 27.8 - - + +
143H ARG* 4.0 11.2 - - + +
146H ALA* 3.5 5.8 - - + +
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Residues in contact with CYS 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G ARG* 3.3 39.7 - - - -
91H GLN* 3.3 6.4 - - - +
92H ASN* 2.9 53.8 + - - -
94H ASP* 4.1 0.4 + - - -
107H VAL* 1.3 75.8 - - - +
109H ALA* 1.3 61.1 + - - +
110H PHE* 3.9 12.8 - - - -
124H VAL* 4.4 6.5 - - + -
125H GLY 3.2 7.6 - - - +
126H TYR* 3.7 19.5 - - + -
146H ALA* 4.0 2.0 - - - -
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Residues in contact with ALA 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ILE* 5.0 1.8 - - + -
90H GLN 3.4 7.6 - - - +
91H GLN* 4.0 11.2 - - + +
108H CYS* 1.3 76.4 - - - +
110H PHE* 1.3 65.5 + - - +
111H VAL* 3.9 6.4 + - + +
123H ASP 3.7 0.3 - - - +
124H VAL* 3.2 4.5 - - - -
125H GLY 2.8 30.9 + - - -
146H ALA* 3.6 31.0 - - + +
147H VAL* 3.8 13.2 - - + +
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Residues in contact with PHE 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ILE* 3.8 30.1 - - + -
91G GLN* 3.2 44.4 - - + -
143G ARG* 4.5 6.5 - - - -
88H ILE* 3.5 5.5 - - - -
89H THR* 2.8 45.0 + - - +
90H GLN* 2.7 42.0 + - + +
92H ASN* 5.6 0.2 - - + -
108H CYS* 3.9 21.5 - - - -
109H ALA* 1.3 73.5 - - - +
111H VAL* 1.3 61.5 + - - +
122H GLU* 3.8 5.6 - - - +
123H ASP 3.4 4.7 - - - +
124H VAL* 3.1 23.3 - - + -
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Residues in contact with VAL 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H HIS* 3.9 25.8 - - + -
87H SER 3.4 11.0 - - - +
88H ILE* 4.5 9.2 - - + -
109H ALA* 4.5 5.8 - - + -
110H PHE* 1.3 79.4 - - - +
112H ARG* 1.3 63.6 + - - +
113H VAL 4.8 0.4 - - - +
122H GLU* 3.2 5.7 - - - +
123H ASP 3.0 30.4 + - - -
147H VAL* 3.7 31.4 - - + +
150H GLY* 3.8 16.4 - - - +
151H LEU* 3.8 21.5 - - + +
154H ALA* 3.8 6.4 - - + +
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Residues in contact with ARG 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G SER* 5.1 5.1 - - - -
86H HIS* 3.0 4.2 - - - -
87H SER* 2.9 44.1 + - - +
89H THR* 3.9 25.5 - - + +
110H PHE 4.2 0.6 + - - -
111H VAL* 1.3 73.2 - - - +
113H VAL* 1.3 63.1 + - - +
114H GLN* 2.9 34.3 + - - +
118H GLY 4.8 0.4 + - - -
120H TYR* 3.6 46.6 - - + +
121H HIS 3.6 6.1 - - - +
122H GLU* 3.8 23.1 - - + -
120I TYR* 5.0 6.0 + - - -
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Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H TRP* 4.0 12.6 - - + -
85H ALA 3.1 14.6 - - - +
86H HIS* 4.0 8.3 - - + +
112H ARG* 1.3 73.9 - - - +
114H GLN* 1.3 67.9 + - - +
120H TYR* 3.2 6.6 - - - +
121H HIS 2.9 41.3 + - - +
151H LEU* 4.7 2.7 - - + -
154H ALA* 3.3 32.1 - - + +
155H LEU* 3.5 25.8 - - + +
158H PHE* 4.0 17.8 - - + -
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Residues in contact with GLN 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PHE* 3.3 15.3 - - + -
27H GLY* 3.5 23.4 - - - -
84H TRP* 3.0 4.0 - - - +
85H ALA 2.7 40.1 + - - +
112H ARG* 2.9 27.1 + - - +
113H VAL* 1.3 77.6 - - - +
115H LEU* 1.3 81.2 + - - +
118H GLY* 3.6 15.0 - - - +
119H SER 3.2 14.8 - - - +
120H TYR* 4.2 3.4 - - + +
120I TYR* 3.3 21.8 + - - +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G TYR* 4.1 13.7 - - + -
26H PHE* 3.3 6.0 - - - -
31H TYR* 3.6 20.4 - - + +
79H PHE* 4.0 18.8 - - + -
83H GLY 3.3 5.2 - - - +
84H TRP* 3.9 18.8 - - + -
113H VAL* 4.9 0.2 - - + -
114H GLN* 1.3 89.7 + - - +
116H LYS* 1.3 53.7 + - - +
117H ASP* 2.8 18.6 + - + -
118H GLY 2.9 12.1 + - - -
119H SER* 2.9 28.2 + - - +
158H PHE* 3.2 48.7 - - + -
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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