Contacts of the strand formed by residues 103 - 115 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96L VAL* 4.3 13.7 - - + -
97L ASP 3.2 15.0 - - - -
98L LEU* 3.8 34.5 - - + -
101L GLY 4.8 2.0 - - - -
102L LYS* 1.3 72.6 - - - +
104L TYR* 1.3 63.7 - - - +
105L VAL* 4.1 4.3 - - + -
129L SER 3.4 6.8 - - - +
131L GLY* 3.0 23.6 + - - -
132L LEU 2.8 11.8 + - - -
133L LYS* 3.3 30.7 - - - -
134L SER 3.9 0.4 - - - -
135L LYS* 3.6 50.3 - - + -
138L SER* 3.7 20.3 + - - +
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Residues in contact with TYR 104 (chain L).
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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95L PHE* 3.2 19.4 - - + -
96L VAL* 3.5 0.5 - - - -
97L ASP* 2.6 47.8 + - + +
99L ASN* 3.9 24.5 - - + +
100L ASN* 3.3 25.0 + - - -
102L LYS* 3.5 34.7 - - + +
103L PHE* 1.3 71.8 - - - +
105L VAL* 1.3 60.6 + - - +
129L SER 3.4 2.7 - - - -
130L GLU* 3.6 31.9 - - + +
131L GLY* 3.7 18.7 - - - -
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Residues in contact with VAL 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L VAL* 4.9 0.2 - - + -
95L PHE* 3.4 14.7 - - - +
96L VAL* 4.2 19.1 - - + -
103L PHE* 4.5 1.8 - - + -
104L TYR* 1.3 84.8 - - - +
106L GLY* 1.3 61.5 + - - +
107L VAL* 4.0 6.5 - - + -
127L GLY 3.7 0.3 - - - +
128L VAL* 3.4 10.7 - - - +
129L SER 2.8 33.9 + - - +
130L GLU* 4.9 1.0 - - - +
135L LYS* 6.3 0.4 - - - -
138L SER* 3.8 30.1 - - - +
139L LEU* 3.6 28.0 - - + +
142L ALA* 3.9 19.0 - - + +
136V ALA* 5.0 0.2 - - - -
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Residues in contact with GLY 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L VAL* 4.0 0.2 - - - -
94L ASP* 2.8 28.1 + - - +
95L PHE* 3.3 22.8 + - - +
105L VAL* 1.3 76.6 - - - +
107L VAL* 1.3 64.7 + - - +
126L TYR* 3.3 24.7 - - - -
127L GLY 3.5 4.3 - - - -
136V ALA* 4.7 0.4 - - - -
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Residues in contact with VAL 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L GLN* 3.7 36.6 - - + +
92L ASN 3.6 12.6 - - - +
93L VAL* 3.8 21.3 - - + -
94L ASP 4.4 0.2 - - - +
105L VAL* 4.0 8.7 - - + -
106L GLY* 1.3 79.3 - - - +
108L CYS* 1.3 64.3 + - - +
126L TYR* 3.2 8.9 - - - -
127L GLY 2.6 37.3 + - - -
139L LEU* 4.7 0.7 - - + -
142L ALA* 3.7 29.4 - - + +
143L ARG* 4.0 11.4 - - + +
146L ALA* 3.5 4.1 - - + +
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Residues in contact with CYS 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L GLN* 3.3 6.4 - - - +
92L ASN* 2.9 48.1 + - - -
107L VAL* 1.3 75.0 - - - +
109L ALA* 1.3 61.9 + - - +
110L PHE* 3.7 20.4 - - - -
124L VAL* 4.5 5.2 - - + -
125L GLY 3.2 8.5 - - - +
126L TYR* 3.6 21.5 - - + -
146L ALA* 4.1 2.0 - - - -
143V ARG* 3.4 38.4 - - - -
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Residues in contact with ALA 109 (chain L).
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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88L ILE* 5.1 1.8 - - + -
90L GLN 3.4 9.4 - - - +
91L GLN* 3.9 14.4 - - + +
108L CYS* 1.3 75.4 - - - +
110L PHE* 1.3 65.8 + - - +
111L VAL* 3.9 6.6 + - + +
123L ASP 3.8 0.3 - - - +
124L VAL* 3.2 4.0 - - - -
125L GLY 2.8 31.5 + - - -
146L ALA 3.7 26.9 - - - +
147L VAL* 3.9 13.2 - - + +
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Residues in contact with PHE 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L ILE* 3.5 5.0 - - - -
89L THR* 2.8 48.2 + - - +
90L GLN* 2.8 40.9 + - + +
92L ASN* 5.6 0.4 - - + -
108L CYS* 3.7 23.8 - - - -
109L ALA* 1.3 72.3 - - - +
111L VAL* 1.3 58.7 + - - +
122L GLU* 3.8 6.7 - - - +
123L ASP 3.4 2.9 - - - +
124L VAL* 3.0 30.7 - - + -
88V ILE* 3.8 31.2 - - + -
91V GLN* 3.3 38.4 - - + -
143V ARG* 4.5 3.8 - - - -
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Residues in contact with VAL 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L HIS* 4.0 25.8 - - + -
87L SER 3.4 12.1 - - - +
88L ILE* 4.7 4.9 - - + -
109L ALA* 4.5 5.4 - - + -
110L PHE* 1.3 77.7 - - - +
112L ARG* 1.3 62.2 + - - +
122L GLU* 3.3 4.0 - - - -
123L ASP 3.1 29.1 + - - -
147L VAL* 3.6 36.6 - - + +
150L GLY* 3.8 16.4 - - - +
151L LEU* 3.7 22.7 - - + +
154L ALA* 3.8 6.7 - - + +
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Residues in contact with ARG 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L HIS* 3.1 4.2 - - - -
87L SER* 2.9 43.8 + - - +
89L THR* 4.0 22.6 - - + +
110L PHE 4.2 0.8 + - - -
111L VAL* 1.3 71.1 - - - +
113L VAL* 1.3 63.9 + - - +
114L GLN* 2.9 34.4 + - - +
118L GLY 4.7 0.8 + - - -
120L TYR* 3.4 48.0 - - + +
121L HIS 3.7 6.1 - - - +
122L GLU* 4.0 24.5 - - + +
120M TYR* 5.0 6.6 + - - -
87V SER* 5.1 4.1 - - - -
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Residues in contact with VAL 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L TRP* 4.1 12.6 - - + -
85L ALA 3.1 12.8 - - - +
86L HIS* 4.0 7.9 - - + +
111L VAL 4.1 0.4 - - - -
112L ARG* 1.3 75.4 - - - +
114L GLN* 1.3 67.3 + - - +
120L TYR* 3.2 7.3 - - - +
121L HIS 2.9 39.9 + - - +
151L LEU* 4.7 3.1 - - + -
154L ALA* 3.4 34.8 - - + +
155L LEU* 3.5 25.8 - - + -
158L PHE* 4.0 16.6 - - + -
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Residues in contact with GLN 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PHE* 3.4 16.0 - - + -
27L GLY* 3.5 17.0 - - - -
84L TRP* 3.1 4.0 - - - +
85L ALA 2.7 39.1 + - - +
112L ARG* 2.9 29.2 + - - +
113L VAL* 1.3 75.6 - - - +
115L LEU* 1.3 80.8 + - - +
118L GLY* 3.5 20.4 - - - +
119L SER 3.2 13.0 - - - +
120L TYR* 4.3 0.2 - - - +
120M TYR* 3.3 22.3 + - - +
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Residues in contact with LEU 115 (chain L).
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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26L PHE* 3.4 4.4 - - - -
31L TYR* 3.6 14.6 - - + +
79L PHE* 4.1 13.0 - - + -
83L GLY 3.3 8.7 - - - +
84L TRP* 3.9 12.6 - - + -
113L VAL* 5.0 0.4 - - + -
114L GLN* 1.3 90.0 + - - +
116L LYS* 1.3 55.1 + - - +
117L ASP* 2.8 8.8 + - + -
118L GLY 2.8 21.8 + - - -
119L SER* 2.8 30.0 + - - +
158L PHE* 3.3 47.8 - - + -
81V TYR* 4.0 24.5 - - + -
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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